Other mistake: When Elastigirl is chasing the high-speed train, as she is in the middle of making her second final jump to reach the train, if one were to look closely, the train actually drives right past her before she lands. (00:31:40)
Other mistake: Violet's date with Tony was on a Friday evening. But the next morning, Mr Incredible sends his kids to school.
Answer: What happened to Syndrome happened high in the air, Elastigirl mentions she can't see whats going on and panics. They never actually see what Jack-Jack is doing and think Syndrome is hurting him.
lionhead